cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2765-Schizophrenia-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2765-Schizophrenia-DLPFC/2765-Schizophrenia-DLPFC.cellbender.output.h5 --cuda --expected-cells 6163 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 91aa9e4c96) cellbender:remove-background: 2024-06-06 15:32:37 cellbender:remove-background: Running remove-background cellbender:remove-background: Loading data from /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2765-Schizophrenia-DLPFC.raw_feature_bc_matrix.h5 cellbender:remove-background: CellRanger v3 format cellbender:remove-background: Features in dataset: 36601 Gene Expression cellbender:remove-background: Trimming features for inference. cellbender:remove-background: 32169 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 5169 cellbender:remove-background: Prior on counts for empty droplets is 62 cellbender:remove-background: Excluding 11873 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 20296 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 31 cellbender:remove-background: Using 6163 probable cell barcodes, plus an additional 13837 barcodes, and 51614 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 62 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpe4tbecja cellbender:remove-background: No saved checkpoint. cellbender:remove-background: No checkpoint loaded. cellbender:remove-background: Running inference... cellbender:remove-background: [epoch 001] average training loss: 6944.7104 cellbender:remove-background: [epoch 002] average training loss: 4908.5254 (6.1 seconds per epoch) cellbender:remove-background: Will checkpoint every 70 epochs cellbender:remove-background: [epoch 003] average training loss: 3996.2805 cellbender:remove-background: [epoch 004] average training loss: 3472.8309 cellbender:remove-background: [epoch 005] average training loss: 3335.7149 cellbender:remove-background: [epoch 005] average test loss: 3416.6734 cellbender:remove-background: [epoch 006] average training loss: 3292.3572 cellbender:remove-background: [epoch 007] average training loss: 3238.3395 cellbender:remove-background: [epoch 008] average training loss: 3201.7870 cellbender:remove-background: [epoch 009] average training loss: 3204.1752 cellbender:remove-background: [epoch 010] average training loss: 3133.0711 cellbender:remove-background: [epoch 010] average test loss: 3104.3097 cellbender:remove-background: [epoch 011] average training loss: 3077.7517 cellbender:remove-background: [epoch 012] average training loss: 3003.7084 cellbender:remove-background: [epoch 013] average training loss: 2968.6719 cellbender:remove-background: [epoch 014] average training loss: 2982.3359 cellbender:remove-background: [epoch 015] average training loss: 2947.6414 cellbender:remove-background: [epoch 015] average test loss: 2954.2877 cellbender:remove-background: [epoch 016] average training loss: 2933.8383 cellbender:remove-background: [epoch 017] average training loss: 2944.8107 cellbender:remove-background: [epoch 018] average training loss: 2931.4252 cellbender:remove-background: [epoch 019] average training loss: 2912.0226 cellbender:remove-background: [epoch 020] average training loss: 2885.1760 cellbender:remove-background: [epoch 020] average test loss: 2894.5804 cellbender:remove-background: [epoch 021] average training loss: 2877.3710 cellbender:remove-background: [epoch 022] average training loss: 2868.2680 cellbender:remove-background: [epoch 023] average training loss: 2850.3215 cellbender:remove-background: [epoch 024] average training loss: 2822.2054 cellbender:remove-background: [epoch 025] average training loss: 2813.0440 cellbender:remove-background: [epoch 025] average test loss: 2785.3621 cellbender:remove-background: [epoch 026] average training loss: 2789.4930 cellbender:remove-background: [epoch 027] average training loss: 2779.9089 cellbender:remove-background: [epoch 028] average training loss: 2777.8708 cellbender:remove-background: [epoch 029] average training loss: 2766.7350 cellbender:remove-background: [epoch 030] average training loss: 2763.6397 cellbender:remove-background: [epoch 030] average test loss: 2744.6210 cellbender:remove-background: [epoch 031] average training loss: 2758.8813 cellbender:remove-background: [epoch 032] average training loss: 2753.8438 cellbender:remove-background: [epoch 033] average training loss: 2752.2903 cellbender:remove-background: [epoch 034] average training loss: 2750.7547 cellbender:remove-background: [epoch 035] average training loss: 2746.6094 cellbender:remove-background: [epoch 035] average test loss: 2725.7857 cellbender:remove-background: [epoch 036] average training loss: 2746.9758 cellbender:remove-background: [epoch 037] average training loss: 2744.3360 cellbender:remove-background: [epoch 038] average training loss: 2742.8056 cellbender:remove-background: [epoch 039] average training loss: 2741.0276 cellbender:remove-background: [epoch 040] average training loss: 2739.7494 cellbender:remove-background: [epoch 040] average test loss: 2717.4161 cellbender:remove-background: [epoch 041] average training loss: 2737.0356 cellbender:remove-background: [epoch 042] average training loss: 2736.5948 cellbender:remove-background: [epoch 043] average training loss: 2733.8902 cellbender:remove-background: [epoch 044] average training loss: 2732.2469 cellbender:remove-background: [epoch 045] average training loss: 2732.7292 cellbender:remove-background: [epoch 045] average test loss: 2699.6982 cellbender:remove-background: [epoch 046] average training loss: 2731.3258 cellbender:remove-background: [epoch 047] average training loss: 2729.5581 cellbender:remove-background: [epoch 048] average training loss: 2729.2021 cellbender:remove-background: [epoch 049] average training loss: 2727.3151 cellbender:remove-background: [epoch 050] average training loss: 2727.2387 cellbender:remove-background: [epoch 050] average test loss: 2696.6551 cellbender:remove-background: [epoch 051] average training loss: 2725.8597 cellbender:remove-background: [epoch 052] average training loss: 2727.2399 cellbender:remove-background: [epoch 053] average training loss: 2727.5638 cellbender:remove-background: [epoch 054] average training loss: 2725.8107 cellbender:remove-background: [epoch 055] average training loss: 2732.4051 cellbender:remove-background: [epoch 055] average test loss: 2731.6026 cellbender:remove-background: [epoch 056] average training loss: 2731.8970 cellbender:remove-background: [epoch 057] average training loss: 2734.7446 cellbender:remove-background: [epoch 058] average training loss: 2730.4857 cellbender:remove-background: [epoch 059] average training loss: 2732.7577 cellbender:remove-background: [epoch 060] average training loss: 2734.5861 cellbender:remove-background: [epoch 060] average test loss: 2710.3337 cellbender:remove-background: [epoch 061] average training loss: 2731.3437 cellbender:remove-background: [epoch 062] average training loss: 2739.1014 cellbender:remove-background: [epoch 063] average training loss: 2732.1989 cellbender:remove-background: [epoch 064] average training loss: 2735.7899 cellbender:remove-background: [epoch 065] average training loss: 2734.4411 cellbender:remove-background: [epoch 065] average test loss: 2734.5982 cellbender:remove-background: [epoch 066] average training loss: 2745.9684 cellbender:remove-background: [epoch 067] average training loss: 2744.5520 cellbender:remove-background: [epoch 068] average training loss: 2730.5224 cellbender:remove-background: [epoch 069] average training loss: 2738.6524 cellbender:remove-background: [epoch 070] average training loss: 2733.1649 cellbender:remove-background: [epoch 070] average test loss: 2737.6415 cellbender:remove-background: Saving a checkpoint... cellbender:remove-background: Saved checkpoint as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2765-Schizophrenia-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 071] average training loss: 2735.2852 cellbender:remove-background: [epoch 072] average training loss: 2735.1142 cellbender:remove-background: [epoch 073] average training loss: 2732.8606 cellbender:remove-background: [epoch 074] average training loss: 2732.8801 cellbender:remove-background: [epoch 075] average training loss: 2724.5041 cellbender:remove-background: [epoch 075] average test loss: 2730.1515 cellbender:remove-background: [epoch 076] average training loss: 2726.0988 cellbender:remove-background: [epoch 077] average training loss: 2732.7217 cellbender:remove-background: [epoch 078] average training loss: 2733.8100 cellbender:remove-background: [epoch 079] average training loss: 2743.2573 cellbender:remove-background: [epoch 080] average training loss: 2727.1017 cellbender:remove-background: [epoch 080] average test loss: 2733.1336 cellbender:remove-background: [epoch 081] average training loss: 2724.1983 cellbender:remove-background: [epoch 082] average training loss: 2734.4832 cellbender:remove-background: [epoch 083] average training loss: 2730.1630 cellbender:remove-background: [epoch 084] average training loss: 2721.3510 cellbender:remove-background: [epoch 085] average training loss: 2737.3267 cellbender:remove-background: [epoch 085] average test loss: 2721.9644 cellbender:remove-background: [epoch 086] average training loss: 2733.0214 cellbender:remove-background: [epoch 087] average training loss: 2732.3609 cellbender:remove-background: [epoch 088] average training loss: 2722.9780 cellbender:remove-background: [epoch 089] average training loss: 2723.0352 cellbender:remove-background: [epoch 090] average training loss: 2723.9646 cellbender:remove-background: [epoch 090] average test loss: 2712.6405 cellbender:remove-background: [epoch 091] average training loss: 2719.4759 cellbender:remove-background: [epoch 092] average training loss: 2720.6437 cellbender:remove-background: [epoch 093] average training loss: 2732.0482 cellbender:remove-background: [epoch 094] average training loss: 2719.6146 cellbender:remove-background: [epoch 095] average training loss: 2720.3967 cellbender:remove-background: [epoch 095] average test loss: 2715.7156 cellbender:remove-background: [epoch 096] average training loss: 2732.2168 cellbender:remove-background: [epoch 097] average training loss: 2717.1101 cellbender:remove-background: [epoch 098] average training loss: 2730.3179 cellbender:remove-background: [epoch 099] average training loss: 2728.3136 cellbender:remove-background: [epoch 100] average training loss: 2719.4092 cellbender:remove-background: [epoch 100] average test loss: 2762.8678 cellbender:remove-background: [epoch 101] average training loss: 2730.4453 cellbender:remove-background: [epoch 102] average training loss: 2719.4551 cellbender:remove-background: [epoch 103] average training loss: 2719.2664 cellbender:remove-background: [epoch 104] average training loss: 2716.6356 cellbender:remove-background: [epoch 105] average training loss: 2715.3515 cellbender:remove-background: [epoch 105] average test loss: 2706.3938 cellbender:remove-background: [epoch 106] average training loss: 2719.4197 cellbender:remove-background: [epoch 107] average training loss: 2718.7432 cellbender:remove-background: [epoch 108] average training loss: 2715.4807 cellbender:remove-background: [epoch 109] average training loss: 2714.0451 cellbender:remove-background: [epoch 110] average training loss: 2723.0668 cellbender:remove-background: [epoch 110] average test loss: 2716.9143 cellbender:remove-background: [epoch 111] average training loss: 2716.0440 cellbender:remove-background: [epoch 112] average training loss: 2717.9680 cellbender:remove-background: [epoch 113] average training loss: 2715.7598 cellbender:remove-background: [epoch 114] average training loss: 2715.1513 cellbender:remove-background: [epoch 115] average training loss: 2720.0088 cellbender:remove-background: [epoch 115] average test loss: 2740.9445 cellbender:remove-background: [epoch 116] average training loss: 2715.5955 cellbender:remove-background: [epoch 117] average training loss: 2719.0983 cellbender:remove-background: [epoch 118] average training loss: 2714.1863 cellbender:remove-background: [epoch 119] average training loss: 2712.8966 cellbender:remove-background: [epoch 120] average training loss: 2719.6516 cellbender:remove-background: [epoch 120] average test loss: 2732.0031 cellbender:remove-background: [epoch 121] average training loss: 2716.3298 cellbender:remove-background: [epoch 122] average training loss: 2705.7104 cellbender:remove-background: [epoch 123] average training loss: 2714.8566 cellbender:remove-background: [epoch 124] average training loss: 2708.9747 cellbender:remove-background: [epoch 125] average training loss: 2711.0134 cellbender:remove-background: [epoch 125] average test loss: 2736.1589 cellbender:remove-background: [epoch 126] average training loss: 2715.7774 cellbender:remove-background: [epoch 127] average training loss: 2712.7945 cellbender:remove-background: [epoch 128] average training loss: 2713.2964 cellbender:remove-background: [epoch 129] average training loss: 2721.0377 cellbender:remove-background: [epoch 130] average training loss: 2707.6955 cellbender:remove-background: [epoch 130] average test loss: 2737.2776 cellbender:remove-background: [epoch 131] average training loss: 2713.2235 cellbender:remove-background: [epoch 132] average training loss: 2707.1384 cellbender:remove-background: [epoch 133] average training loss: 2712.5988 cellbender:remove-background: [epoch 134] average training loss: 2710.3107 cellbender:remove-background: [epoch 135] average training loss: 2710.2968 cellbender:remove-background: [epoch 135] average test loss: 2775.0261 cellbender:remove-background: [epoch 136] average training loss: 2717.6140 cellbender:remove-background: [epoch 137] average training loss: 2708.1722 cellbender:remove-background: [epoch 138] average training loss: 2716.0627 cellbender:remove-background: [epoch 139] average training loss: 2713.1848 cellbender:remove-background: [epoch 140] average training loss: 2710.3326 cellbender:remove-background: [epoch 140] average test loss: 2725.1365 cellbender:remove-background: Saving a checkpoint... cellbender:remove-background: Saved checkpoint as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2765-Schizophrenia-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 141] average training loss: 2709.6565 cellbender:remove-background: [epoch 142] average training loss: 2709.3719 cellbender:remove-background: [epoch 143] average training loss: 2709.9178 cellbender:remove-background: [epoch 144] average training loss: 2705.7615 cellbender:remove-background: [epoch 145] average training loss: 2722.0188 cellbender:remove-background: [epoch 145] average test loss: 2724.9202 cellbender:remove-background: [epoch 146] average training loss: 2710.0504 cellbender:remove-background: [epoch 147] average training loss: 2707.4942 cellbender:remove-background: [epoch 148] average training loss: 2705.9369 cellbender:remove-background: [epoch 149] average training loss: 2717.5854 cellbender:remove-background: [epoch 150] average training loss: 2706.7349 cellbender:remove-background: [epoch 150] average test loss: 2729.5947 cellbender:remove-background: Saving a checkpoint... cellbender:remove-background: Saved checkpoint as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2765-Schizophrenia-DLPFC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:51:08 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpth3e1z2w cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpth3e1z2w /tmp/tmpth3e1z2w/91aa9e4c96_random.pyro /tmp/tmpth3e1z2w/91aa9e4c96_random.cuda /tmp/tmpth3e1z2w/91aa9e4c96_model.torch /tmp/tmpth3e1z2w/91aa9e4c96_optim.torch /tmp/tmpth3e1z2w/91aa9e4c96_optim.pyro /tmp/tmpth3e1z2w/91aa9e4c96_params.pyro /tmp/tmpth3e1z2w/91aa9e4c96_train.loaderstate /tmp/tmpth3e1z2w/91aa9e4c96_test.loaderstate /tmp/tmpth3e1z2w/91aa9e4c96_args.npy cellbender:remove-background: Posterior not currently included in checkpoint. cellbender:remove-background: Computing posterior noise count probabilities in mini-batches. cellbender:remove-background: Working on chunk (1/59) cellbender:remove-background: [0.03 mins per chunk] cellbender:remove-background: Working on chunk (2/59) cellbender:remove-background: Working on chunk (3/59) cellbender:remove-background: Working on chunk (4/59) cellbender:remove-background: Working on chunk (5/59) cellbender:remove-background: Working on chunk (6/59) cellbender:remove-background: Working on chunk (7/59) cellbender:remove-background: Working on chunk (8/59) cellbender:remove-background: Working on chunk (9/59) cellbender:remove-background: Working on chunk (10/59) cellbender:remove-background: Working on chunk (11/59) cellbender:remove-background: Working on chunk (12/59) cellbender:remove-background: Working on chunk (13/59) cellbender:remove-background: Working on chunk (14/59) cellbender:remove-background: Working on chunk (15/59) cellbender:remove-background: Working on chunk (16/59) cellbender:remove-background: Working on chunk (17/59) cellbender:remove-background: Working on chunk (18/59) cellbender:remove-background: Working on chunk (19/59) cellbender:remove-background: Working on chunk (20/59) cellbender:remove-background: Working on chunk (21/59) cellbender:remove-background: Working on chunk (22/59) cellbender:remove-background: Working on chunk (23/59) cellbender:remove-background: Working on chunk (24/59) cellbender:remove-background: Working on chunk (25/59) cellbender:remove-background: Working on chunk (26/59) cellbender:remove-background: Working on chunk (27/59) cellbender:remove-background: Working on chunk (28/59) cellbender:remove-background: Working on chunk (29/59) cellbender:remove-background: Working on chunk (30/59) cellbender:remove-background: Working on chunk (31/59) cellbender:remove-background: Working on chunk (32/59) cellbender:remove-background: Working on chunk (33/59) cellbender:remove-background: Working on chunk (34/59) cellbender:remove-background: Working on chunk (35/59) cellbender:remove-background: Working on chunk (36/59) cellbender:remove-background: Working on chunk (37/59) cellbender:remove-background: Working on chunk (38/59) cellbender:remove-background: Working on chunk (39/59) cellbender:remove-background: Working on chunk (40/59) cellbender:remove-background: Working on chunk (41/59) cellbender:remove-background: Working on chunk (42/59) cellbender:remove-background: Working on chunk (43/59) cellbender:remove-background: Working on chunk (44/59) cellbender:remove-background: Working on chunk (45/59) cellbender:remove-background: Working on chunk (46/59) cellbender:remove-background: Working on chunk (47/59) cellbender:remove-background: Working on chunk (48/59) cellbender:remove-background: Working on chunk (49/59) cellbender:remove-background: Working on chunk (50/59) cellbender:remove-background: Working on chunk (51/59) cellbender:remove-background: Working on chunk (52/59) cellbender:remove-background: Working on chunk (53/59) cellbender:remove-background: Working on chunk (54/59) cellbender:remove-background: Working on chunk (55/59) cellbender:remove-background: Working on chunk (56/59) cellbender:remove-background: Working on chunk (57/59) cellbender:remove-background: Working on chunk (58/59) cellbender:remove-background: Working on chunk (59/59) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2765-Schizophrenia-DLPFC/2765-Schizophrenia-DLPFC.cellbender.output_posterior.h5 cellbender:remove-background: Succeeded in writing posterior to file /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2765-Schizophrenia-DLPFC/2765-Schizophrenia-DLPFC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:54:43 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2765-Schizophrenia-DLPFC/2765-Schizophrenia-DLPFC.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2765-Schizophrenia-DLPFC/2765-Schizophrenia-DLPFC.cellbender.output_cell_barcodes.csv cellbender:remove-background: Computing target noise counts per gene for MCKP estimator cellbender:remove-background: Using MCKP noise targets computed for FPR 0.01 cellbender:remove-background: Computing denoised counts using mckp estimator cellbender:remove-background: Working on chunk (1/7) cellbender:remove-background: [1.32 mins per chunk] cellbender:remove-background: Working on chunk (2/7) cellbender:remove-background: Working on chunk (3/7) cellbender:remove-background: Working on chunk (4/7) cellbender:remove-background: Working on chunk (5/7) cellbender:remove-background: Working on chunk (6/7) cellbender:remove-background: Working on chunk (7/7) cellbender:remove-background: 2024-06-06 16:04:13 Total MCKP estimation time = 546.87 sec cellbender:remove-background: Succeeded in writing CellRanger format output to file /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2765-Schizophrenia-DLPFC/2765-Schizophrenia-DLPFC.cellbender.output.h5 cellbender:remove-background: Succeeded in writing CellRanger format output to file /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2765-Schizophrenia-DLPFC/2765-Schizophrenia-DLPFC.cellbender.output_filtered.h5 cellbender:remove-background: Saved output metrics as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2765-Schizophrenia-DLPFC/2765-Schizophrenia-DLPFC.cellbender.output_metrics.csv Traceback (most recent call last): File "/home/users/guozy/miniconda3/envs/cellbender/bin/jupyter-nbconvert", line 5, in from nbconvert.nbconvertapp import main File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/__init__.py", line 5, in from .exporters import * File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/__init__.py", line 1, in from .asciidoc import ASCIIDocExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/asciidoc.py", line 9, in from .templateexporter import TemplateExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 25, in from lxml.html.clean import clean_html File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/lxml/html/clean.py", line 21, in ) from None ImportError: lxml.html.clean module is now a separate project lxml_html_clean. Install lxml[html_clean] or lxml_html_clean directly. Traceback (most recent call last): File "/home/users/guozy/miniconda3/envs/cellbender/bin/jupyter-nbconvert", line 5, in from nbconvert.nbconvertapp import main File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/__init__.py", line 5, in from .exporters import * File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/__init__.py", line 1, in from .asciidoc import ASCIIDocExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/asciidoc.py", line 9, in from .templateexporter import TemplateExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 25, in from lxml.html.clean import clean_html File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/lxml/html/clean.py", line 21, in ) from None ImportError: lxml.html.clean module is now a separate project lxml_html_clean. Install lxml[html_clean] or lxml_html_clean directly. mv: cannot stat ‘tmp.report.nbconvert.html’: No such file or directory rm: cannot remove ‘tmp.report.nbconvert.ipynb’: No such file or directory cellbender:remove-background: Unable to create report. cellbender:remove-background: Traceback (most recent call last): File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/run.py", line 351, in compute_output_denoised_counts_reports_metrics output=html_report_file, File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/report.py", line 82, in run_notebook_make_html title=('CellBender: ' + os.path.basename(output).replace('_report.html', '')), File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/report.py", line 59, in _postprocess_html with open(file, mode='r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2765-Schizophrenia-DLPFC/2765-Schizophrenia-DLPFC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 16:04:29